\documentclass[12pt]{article}
\usepackage[margin=1.0in]{geometry}
\title{Extended Sweave Example}
\author{Theresa A Scott, MS}
\date{ }
\SweaveOpts{prefix.string=graphics/plot} % Created a "graphics" subdirectory to save graph files in
\begin{document}
\maketitle

% Hidden R code chunk --- reading in the data
<<echo = false, results = hide>>=
library(xtable)
data(mtcars)
names(mtcars)
@

\section{Analysis \& Results}
The \texttt{mtcars} (`Motor Trend Car Road Tests') data set is comprised of \Sexpr{ncol(mtcars)} aspects of automobile design and performance (columns) for \Sexpr{nrow(mtcars)} automobiles (rows).  We wish to know if there is a significant difference in the quarter mile track times (\texttt{qsec}) between the different cylinder classes (\texttt{cyl}; 4, 6, and 8).\\

\noindent Let's first examine the quantiles (minumum, first quantile, median, and third quantile) of the times within each cylinder class.  These value are given in Table \ref{table:quantiles}.

% R code chunk that generates LaTeX code to create table
<<echo = false, results = tex>>=
tabledf <- data.frame("N.cylinders" = sort(unique(mtcars$cyl)),
   "Min" = with(mtcars, tapply(X = qsec, INDEX = list(cyl), FUN = min, na.rm = TRUE)),
   "Q1" = with(mtcars, tapply(X = qsec, INDEX = list(cyl), FUN = quantile, prob = 0.25, na.rm = TRUE)),
   "Median" = with(mtcars, tapply(X = qsec, INDEX = list(cyl), FUN = median, na.rm = TRUE)),
   "Q3" = with(mtcars, tapply(X = qsec, INDEX = list(cyl), FUN = quantile, prob = 0.75, na.rm = TRUE)),
   "Max" = with(mtcars, tapply(X = qsec, INDEX = list(cyl), FUN = max, na.rm = TRUE)))
print(xtable(tabledf, caption = "Quantiles of the quarter mile track times within each cylinder class",
   label = "table:quantiles"), caption.placement = "top", include.rownames = FALSE)
@

\noindent Based on a non-parametric Kruskal-Wallis test, we see that the times are significantly different from each other:
<<>>=
with(mtcars, kruskal.test(qsec ~ cyl))
@

% Hidden R code chunk that assigns objects that contain calculated values to be used in \Sexpr{}
%	statements in following paragraph
% NOTE: The objects are assigned in this code chunk because the R code in the \Sexpr{} statement
%	would break over multiple lines.
<<echo = false, results = hide>>=
n4cyl <- nrow(subset(mtcars, cyl == 4))
n6cyl <- nrow(subset(mtcars, cyl == 6))
n8cyl <- nrow(subset(mtcars, cyl == 8))

prop4cyl <- format(round(nrow(subset(mtcars, cyl == 4))/nrow(mtcars)*100, 1), nsmall = 1)
prop6cyl <- format(round(nrow(subset(mtcars, cyl == 6))/nrow(mtcars)*100, 1), nsmall = 1)
prop8cyl <- format(round(nrow(subset(mtcars, cyl == 8))/nrow(mtcars)*100, 1), nsmall = 1)

@

\noindent Lastly, Figure \ref{figure:boxstrip} graphically displays the distribution of the times within each cylinder class -- the raw values (shown using a `stripchart') are overlaid with side-by-side boxplots.  The width of each box is also proportional to the number of cars within each cylinder group -- 
\Sexpr{prop4cyl}\% (\Sexpr{n4cyl}) 4 cyclinder cars; \Sexpr{prop6cyl}\% (\Sexpr{n6cyl}) 6 cyclinder cars; and \Sexpr{prop8cyl}\% (\Sexpr{n8cyl}) 8 cyclinder cars. 
% First a hidden R code chunk that adds some labels to certain variables --- to be referenced in plot
<<echo = false, results = hide>>=
library(Hmisc)
label(mtcars$qsec) <- "1/4 mile track time (sec)"
label(mtcars$cyl) <- "No. of cylinders"
@

% Additional LaTeX code to add caption to figure
\begin{figure}\label{figure:boxstrip}
\caption{Distribution of 1/4 mile track time (sec) within each cylinder class.}
\begin{center}
\setkeys{Gin}{width=0.75\textwidth} % LaTeX code to read the graphic file in at 75% of its original size
% R code chunk that produces a graphic
<<echo = false, fig = true>>=
with(mtcars, {
   boxplot(qsec ~ cyl, outpch = NA, varwidth = TRUE,  xlab = label(cyl), ylab = label(qsec),
      main = paste("Boxplot of", label(qsec), "by\n", label(cyl)))
   stripchart(qsec ~ cyl, method = "jitter", pch = 1, vertical = TRUE, add = TRUE)
})
box("figure") # Adds box around figure
@
\end{center}
\end{figure}

\end{document}